bmtk.utils package

Subpackages

Submodules

bmtk.utils.hdf5_helper module

bmtk.utils.hdf5_helper.get_attribute_h5(h5obj, attribut_name, default=None)[source]

bmtk.utils.sim_setup module

class bmtk.utils.sim_setup.BioNetEnvBuilder(base_dir='.', network_dir=None, components_dir=None, output_dir=None, node_sets_file=None)[source]

Bases: bmtk.utils.sim_setup.EnvBuilder

property bmtk_simulator
compile_mechanisms()[source]
property examples_dir
property target_simulator
class bmtk.utils.sim_setup.EnvBuilder(base_dir='.', network_dir=None, components_dir=None, output_dir=None, node_sets_file=None)[source]

Bases: object

property base_dir
property bmtk_simulator
build(include_examples=False, use_relative_paths=True, report_vars=[], report_nodes=None, clamp_reports=[], current_clamp=None, file_current_clamp=None, se_voltage_clamp=None, spikes_inputs=None, config_file='config.json', overwrite_config=False, **run_args)[source]
property components_dir
property examples_dir
property network_dir
property node_sets_file
property output_dir
property scripts_root
property target_simulator
class bmtk.utils.sim_setup.FilterNetEnvBuilder(base_dir='.', network_dir=None, components_dir=None, output_dir=None, node_sets_file=None)[source]

Bases: bmtk.utils.sim_setup.EnvBuilder

property bmtk_simulator
property examples_dir
property target_simulator
class bmtk.utils.sim_setup.PointNetEnvBuilder(base_dir='.', network_dir=None, components_dir=None, output_dir=None, node_sets_file=None)[source]

Bases: bmtk.utils.sim_setup.EnvBuilder

property bmtk_simulator
property examples_dir
property target_simulator
class bmtk.utils.sim_setup.PopNetEnvBuilder(base_dir='.', network_dir=None, components_dir=None, output_dir=None, node_sets_file=None)[source]

Bases: bmtk.utils.sim_setup.EnvBuilder

property bmtk_simulator
property examples_dir
property target_simulator
bmtk.utils.sim_setup.build_env_bionet(base_dir='.', network_dir=None, components_dir=None, node_sets_file=None, include_examples=False, overwrite_config=False, tstart=0.0, tstop=1000.0, dt=0.001, dL=20.0, spikes_threshold=- 15.0, nsteps_block=5000, v_init=- 80.0, celsius=34.0, report_vars=[], report_nodes=None, clamp_reports=[], current_clamp=None, file_current_clamp=None, se_voltage_clamp=None, spikes_inputs=None, compile_mechanisms=False, use_relative_paths=True, config_file=None)[source]
bmtk.utils.sim_setup.build_env_filternet(base_dir='.', network_dir=None, components_dir=None, node_sets_file=None, include_examples=False, tstart=0.0, tstop=1000.0, config_file='config.json')[source]
bmtk.utils.sim_setup.build_env_pointnet(base_dir='.', network_dir=None, components_dir=None, node_sets_file=None, include_examples=False, tstart=0.0, tstop=1000.0, dt=0.001, dL=20.0, spikes_threshold=- 15.0, nsteps_block=5000, v_init=- 80.0, celsius=34.0, report_vars=[], report_nodes=None, current_clamp=None, spikes_inputs=None, use_relative_paths=True, config_file=None)[source]
bmtk.utils.sim_setup.build_env_popnet(base_dir='.', network_dir=None, components_dir=None, node_sets_file=None, reports=None, include_examples=True, config_file=None, tstart=0.0, tstop=1000.0, dt=0.001, **args)[source]

Module contents